#
#	create bedgraph for 317 kb alpha globin region on chromosome 11 chr11:31991635-32308398
#

#
#   A/J
#
bamtools filter -in data/WTCHG_10808.bam -region "chr11:31991635-32308398" -out display_on_ucsc/aj.chr11_region.bam
echo "track type=bedGraph name=track_label description=center_label color=255,0,0" > display_on_ucsc/aj.chr11_region.bedgraph
genomeCoverageBed -bg -ibam display_on_ucsc/aj.chr11_region.bam -g display_on_ucsc/genome_sizes_from_ucsc.data >> display_on_ucsc/aj.chr11_region.bedgraph
python compress_bedgraph.py -i display_on_ucsc/aj.chr11_region.bedgraph -o display_on_ucsc/aj.chr11_region.compressed.bedgraph

#
#   AKR
#
bamtools filter -in data/WTCHG_14213.bam -region "chr11:31991635-32308398" -out display_on_ucsc/akr.chr11_region.bam
echo "track type=bedGraph name=track_label description=center_label color=0,0,255" > display_on_ucsc/akr.chr11_region.bedgraph
genomeCoverageBed -bg -ibam display_on_ucsc/akr.chr11_region.bam -g display_on_ucsc/genome_sizes_from_ucsc.data >> display_on_ucsc/akr.chr11_region.bedgraph
python compress_bedgraph.py -i display_on_ucsc/akr.chr11_region.bedgraph -o display_on_ucsc/akr.chr11_region.compressed.bedgraph
